D'uh!!! I need to get used to always "ray" before assuming anything.
Sorry for the noise! -----Original Message----- From: Justin Lecher [mailto:j.lec...@fz-juelich.de] Sent: Tuesday, August 26, 2014 4:24 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] cartoon_transparency issue On 25/08/14 18:42, Markus Heller wrote: > Hello, > > Attached is a crop of a figure create with the latest PyMOL under Windoze 7 > 64 bit. When setting cartoon_transparency, I get a gray band on the > cartoons. Where does this come from, and how do I get rid of it? > > Thanks and Cheers > Markus > > Here's my code: > > # reset everything > delete all > > # white background > bg_color white > > # show valences > set valence, 1 > > # show valences inside rings, 0 = centered, 1 = inside set valence_mode, 1 > > # antialias > set antialias = 1 > > # load the PDB files > > load ... example PDB > > # turn on grid mode and set it up > set grid_mode, 1 > > # hide everything > hide everything > > # select protein > select prot, polymer > > # color everything > color white > > # show cartoon ribbon for protein > show cartoon > > # don't show backbone for cartoons > set cartoon_side_chain_helper, on > > # keep standard helix, strand, loop representations # other options: cartoon > loop, cartoon rect, # cartoon oval , cartoon tube cartoon automatic > > # color cartoon white and set transparency set cartoon_color, white set > cartoon_transparency, 0.7 > > # select residue of interest > select roi, resi 27+31+34+37+41 > > # show sticks for ROIs > show sticks, roi > > # hide non-polar H > hide (h. and (e. c extend 1)) > > # color ROIs > color atomic > color yellow, (name C* and roi) > > # show H-bonds between sidechains and assign to slots dist Hbo-sc, resi 37, > resi 41, mode = 2 > > # hide alls labels > hide labels > > # color all dashes green > set dash_color, green > > # deselect all to avoid little pink squares deselect > > > > > ------------------------------------------------------------------------------ > Slashdot TV. > Video for Nerds. Stuff that matters. > http://tv.slashdot.org/ > > > > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Hi markus, just raytrace you figure using the "ray" command. Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
